.PHONY : check clean benchmark

benchmark: output.fasta protein.fasta codonfreq.txt
	@echo "\nRUNNING BENCHMARKS\n------------------"
	@echo 'Codon spacing (maximize):'
	@benchmark/AvgCodonSpacing.pl output.fasta
	@echo 'Deviation from the codon frequency table (minimize):'
	@benchmark/CodonFreqStdDev.pl benchmark/tests/HumanCodonFreq.txt output.fasta
	@echo 'Pairwise ID between sequences in output.fasta (minimize):'
	@benchmark/PairID.pl output.fasta
	@echo 'Pairwise ID between sequence in protein.fasta and sequences in output.fasta (should be as close as possible to X in params.txt):'
	@benchmark/SeedStatistics.pl protein.fasta output.fasta
	@echo "\n"

check:
	@echo 'tests not yet implemented'

clean:
	@echo 'nothing to clean' 
